1YF2

Three-dimensional structure of DNA sequence specificity (S) subunit of a type I restriction-modification enzyme and its functional implications

Summary for 1YF2

• Entry DOI: 10.2210/pdb1yf2/pdb
• Descriptor: Type I restriction-modification enzyme, S subunit (2 entities in total)
• Functional Keywords: type i restriction modification enzyme, s-subunit, structural genomics, psi, protein structure initiative, berkeley structural genomics center, bsgc, hydrolase regulator
• Biological source: Methanocaldococcus jannaschii
• Total number of polymer chains: 2
• Total formula weight: 97279.11

Authors

Kim, J.S.,Degiovanni, A.,Jancarik, J.,Adams, P.D.,Yokota, H.A.,Kim, R.,Kim, S.H.,Berkeley Structural Genomics Center (BSGC) (deposition date: 2004-12-30, release date: 2005-02-15, Last modification date: 2024-02-14)

Primary citation

Kim, J.S.,Degiovanni, A.,Jancarik, J.,Adams, P.D.,Yokota, H.,Kim, R.,Kim, S.H.
Crystal structure of DNA sequence specificity subunit of a type I restriction-modification enzyme and its functional implications.
Proc.Natl.Acad.Sci.USA, 102:3248-3253, 2005

PubMed Abstract: Type I restriction-modification enzymes are differentiated from type II and type III enzymes by their recognition of two specific dsDNA sequences separated by a given spacer and cleaving DNA randomly away from the recognition sites. They are oligomeric proteins formed by three subunits: a specificity subunit, a methylation subunit, and a restriction subunit. We solved the crystal structure of a specificity subunit from Methanococcus jannaschii at 2.4-A resolution. Two highly conserved regions (CRs) in the middle and at the C terminus form a coiled-coil of long antiparallel alpha-helices. Two target recognition domains form globular structures with almost identical topologies and two separate DNA binding clefts with a modeled DNA helix axis positioned across the CR helices. The structure suggests that the coiled-coil CRs act as a molecular ruler for the separation between two recognized DNA sequences. Furthermore, the relative orientation of the two DNA binding clefts suggests kinking of bound dsDNA and exposing of target adenines from the recognized DNA sequences.

PubMed: 15728358
DOI: 10.1073/pnas.0409851102

Experimental method

X-RAY DIFFRACTION (2.4 Å)